Plot twist: Brenda works for WICKED.
That's right, the Crank girl Thomas finds in the Scorch is yet another Variable—another trick—supplied by the good folks at WICKED. Luckily for Thomas, Brenda hates WICKED just as much as he does. She's also an Immune with lots of information about WICKED, so she comes in handy.
Brenda's functionality is this book can really be boiled down to that of a key: she helps Thomas get to the places he needs to go, and she helps him survive. Plus, Thomas totally has the hots for her, so we can assume they live happily ever after with each other. (Teresa who?)
Though we can't trust anyone in this series, Brenda does seem sincere when she tells Thomas, "I hate these people just as much as you" (12.28). Later, Brenda really does open up about her experience in the Scorch, and this draws her even closer to Thomas: "I was there on a job, I was there to help things play out, but I did grow close to you and it did change me. And there are a few things I think you deserve to know. About me..." (29.12).
Brenda wants to tell Thomas about her whole purpose in WICKED's experiment, but Thomas doesn't want to be spoon-fed any more lies. When she says, "I think you deserve to know," Brenda's actually trying to confess her final secret: that she's been sent by Chancellor Paige to get Thomas to paradise. Hey, at least she tries to come clean.
Overall, though—aside from the whole fact that she's still technically carrying out an order by WICKED—Brenda is a helper. She's a key, and without her, Thomas and the others would never even get close to reaching paradise. As Thomas says, "Brenda thought before she acted, and that was what they needed to get out of this alive" (47.9).
He couldn't hit the nail on the head any harder than that.